A rod holder mounting system including first and second mounting bracket sub-assemblies adapted to couple to first and second opposing ends of a rod holder sub-assembly. The first and second mounting bracket sub-assemblies respectively couple to first and second opposing ones of a vehicle's existing tie down bracket coupling locations, existing tie down brackets, or a tool box, and the rod holder sub-assembly includes a cross bar with rod holder tubes and first and second locking systems adapted to removably couple the cross bar to the first and second mounting bracket sub-assemblies, respectively. The rod holder mounting system allows for the transportation of fishing rods and reels in a vehicle and locks both the rod holder sub-assembly to the vehicle and the rods and reels to the mounting system.